In recent years, groundwater fluctuations and rising of Parsabad plain in recent years has resulted in the formation of some problems such as water logging and salinity of agricultural lands as well as in the destruction of rural and urban's building foundations and in the subsidence of roads and building. In this research, considering geomorphology features and the style of their effects on groundwater fluctuations by means of Geographical Information System (GIS), the trend of groundwater was modeled so that the effect of groundwater fluctuation can be minimized by change in irrigation system. The monthly data of 30 observational well, geological, topographical, climatic data, soil and territorial recourses of study area was used for surveying the level of groundwater fluctuations. Using the 2002 to 2008 period data, trend of groundwater fluctuation and hydrograph level were drawn. Then the relationship between different geographic factors and groundwater fluctuation were evaluated. Pearson correlation and linear multivariate regression model between effective parameters in groundwater fluctuation and were prepared, in which operation criteria in test course shows adequate performance of mentioned model. The obtained results imply the increase in groundwater level of plain and that its flow is from south to north especially northeast. It was found that, among factors, elevation, slope, earth material (porosity and transition capacity) are highly effective, permeability, precipitation and evaporation are less effective in groundwater fluctuation whereas the depth of groundwater doesn’t have any effect on groundwater fluctuation. Operating continuous draining in most part of plain and modifying irrigation system from traditional to mechanized system can prevent the salinity of cultivated soils and the subsidence of some homes.